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Improving interoperability between microbial information and sequence databases
2005
BMC Bioinformatics
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Identification of links to sequence databases can be useful, but annotation and indexing problems, together with compilation errors, immediately arise. ...
Conclusion: Links between EMBL and CABRI catalogues constitute an improved access to microorganisms of certified quality and can produce positive effects on biomedical research. ...
Acknowledgements This work was partially supported by the "European Biological Resource Centres Network" project, funded by the European Union in the frame of the "Quality of life and management of living ...
doi:10.1186/1471-2105-6-s4-s23
pmid:16351750
pmcid:PMC1866384
fatcat:dovfpewrqfhv3nhbkbtlntg6va
An Information System for European culture collections: the way forward
2016
SpringerPlus
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Users primarily noted that databases were not interoperable, thus rendering a global search of multiple databases impossible. ...
Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently. ...
Analysis of the data provision requests from users can be separated into two main categories: (1) availability of improved and reliable metadata, and (2) improved interoperability between databases. ...
doi:10.1186/s40064-016-2450-8
pmid:27386258
pmcid:PMC4912550
fatcat:sckraiy3wzh6jfsb4u5jpcyj6q
Report On Workshop And Surveys On Current Collection Status Of Data Management Systems, Metadata Sources, Semantic Systems, And Molecular, Taxonomy, Nomenclature, Bibliography And Environmental Databases To Be Considere D By The Platform
2014
Zenodo
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management of and an advanced access to culture collection data, - the information systems that relate to the microbiological domain and should interoperate with the MIRRI-IS. ...
In the first report, deliverable D8.1, the MIRRI Information System (MIRRI-IS) vision and strategy was introduced. ...
Public databases and information systems related to microbial resources Many public information systems and databases exist that may support, in tight connection with mBRC databases, the proposed downstream ...
doi:10.5281/zenodo.154637
fatcat:cx3kouposzcirll2w5ukhfxn4e
Micado—a network-oriented database for microbial genomes
1997
Bioinformatics
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It links eubacterial and archaeal sequences, genetic maps for Bacillus subtilis and Escherichia coli, and information on mutants. ...
We have automated imports of microbial sequences, and E.coli genetic map, by programming parsers of flat file distributions. ...
Acknowledgements We thank Dusko Ehrlich for his active support and contribution to the project, Shahinaz Gas and Jakub Zimmermann, students involved in the development of the database, the B.subtilis community ...
doi:10.1093/bioinformatics/13.4.431
fatcat:rmmqim4m65a7dinbo4wpkeebdy
The MAR databases: development and implementation of databases specific for marine metagenomics
2017
Nucleic Acids Research
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Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. ...
All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. ...
ACKNOWLEDGEMENTS We thank all the experts who contributed to the MMP database annotations from their field of expertise, especially ELIXIR EXCELERATE WP6 partners. ...
doi:10.1093/nar/gkx1036
pmid:29106641
pmcid:PMC5753341
fatcat:wgg4tz754zcebam7dvtoddoawm
Bioinformatics activities at the University Hospital San Martino IST in Genoa
2017
EMBnet journal
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When the EMBL Nucleotide Sequence Data Library was first established, in 1980, the challenges mainly related to establishing the first databases and developing sequence comparison algorithms. ...
With SRS, data must reside locally and be stored in 'flat files' (text-only files) with pre-defined, shared syntaxes. Both explicit and implicit links between databases can be defined. ...
doi:10.14806/ej.23.0.884
fatcat:x534vlgbezcd5mainfea57cylu
Skerman and beyond: 2019 status of the Global Catalogue of Microorganisms
2019
Microbiology Australia
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As a result, the WDCM is now facilitating the application of cutting-edge information technology to improve the interoperability of microbial data, promote the access to and use of data and information ...
In the advance stage of the GCM 2 development the following points are targeted: (1) From strain data to 'omics' data and to improved database platform, (2) from database to knowledge base and to improved ...
doi:10.1071/ma19033
fatcat:oql27avhy5dsvct6ulabm2orhi
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges
2016
Database: The Journal of Biological Databases and Curation
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of mining information from millions of full-text articles, (ii) the 'interoperability' issue of integrating various text-mining systems into existing curation workflows and (iii) the 'reusability' issue ...
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. ...
Figure 1 . 1 Interconnection between literature services and biological databases. ...
doi:10.1093/database/baw161
pmid:28025348
pmcid:PMC5199160
fatcat:q22gw7owfjejznsrom3c4xnlem
Improving the quality and workflow of bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform
2018
Swiss Medical Weekly
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In addition, high quality sequence data are a key element between centres using WGS data for diagnostic and epidemiological applications. ...
However, the transmission between compartments (human, animal, food, environment) is very complex. Interoperable and curated metadata are a key requirement for fully understanding this complexity. ...
, initiatives, and analytical tools using whole genome sequence information from pathogens Weblink
Database
Global microbial identifier http://www.globalmicrobialidentifier.org
Compare
http://www.compare-europe.eu ...
doi:10.4414/smw.2018.14693
fatcat:fb2rjqb7jncvpnx4p4tve7hmsq
The next meta-challenge for Bioinformatics
2008
Bioinformation
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The direct sequencing of uncultivable organisms present in complex biological and environmental samples has opportunities to discover new life forms and metabolic processes. ...
metagenomic information into biomedical, agricultural, environmental, and industrial applications. ...
Mya Breitbart and Francis Larson for the insightful comments and suggestions. The genomic barcoding technology is partially supported by the Defense Threat Reduction Agency. ...
doi:10.6026/97320630002358
pmid:18685725
pmcid:PMC2478737
fatcat:vcivjjwhcjf3leqgy4sw4qov7m
Bacterial genome sequencing and analysis: paving the way for a Switzerland-wide molecular epidemiological surveillance platform
2019
Swiss Medical Weekly
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Interoperable and curated metadata area key requirement for fully understanding this complexity.In addition, high quality sequence data are a key elementbetween centres using WGS data for diagnostic and ...
Thespread of highly virulent and resistant pathogens can bedescribed using molecular typing technologies; in particu-lar, whole genome sequencing (WGS) data can be usedfor molecular typing purposes with ...
, initiatives, and analytical tools using whole genome sequence information from pathogens Weblink
Database
Global microbial identifier http://www.globalmicrobialidentifier.org
Compare
http://www.compare-europe.eu ...
doi:10.4414/smw.2019.14707
fatcat:ujwfozpemvctzellzzwfit5cpi
BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis
2018
Nucleic Acids Research
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With its current release (7/2018) the database offers information for 63 669 bacterial and archaeal strains including 12 715 type strains. ...
A revised graphical user interface and new search tools such as the API® test finder, the TAXplorer, or the Microbial Isolation Source Search significantly improve the user experience. ...
On the data level, interoperability is attained by applying standards and stable identifiers like INSDC sequence accession numbers (10) for sequence data, culture collection numbers for microbial strains ...
doi:10.1093/nar/gky879
pmid:30256983
pmcid:PMC6323973
fatcat:eq6b3t4o7nennldlg5n6db4imy
D8.4_Mirri_Report On Comparison Of Various Integration Software Operating In Life Sciences
2015
Zenodo
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The objective of this deliverable is the analysis of some data integration architectures and tools in Life Sciences to determine their respective advantages and disadvantages in meeting the objectives ...
two sections: 'Get microbial data' and 'Retrieve external information'. ...
Thanks to the inclusion of nucleotide and protein sequences in GCM, sequence alignments between various strains, generally at species level, are possible. ...
doi:10.5281/zenodo.49968
fatcat:72fy55qtjfgbrecrkslp25s5he
Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens
2020
One Health Outlook
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Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow. ...
And finally, we provide curation guidance and an SOP for keeping your public data current within the database. ...
We also thank our Genometrakr collaborators (including CDC, FSIS, NCBI, and David Lipman) for reviewing the manuscript and providing feedback prior to publication. ...
doi:10.1186/s42522-020-00026-3
pmid:33103064
pmcid:PMC7568946
fatcat:yfexo6xtobcm3ffw3gexlxlg2u
ELIXIR-EXCELERATE D6.5: Improvement and Application of Eukaryotic Gene catalogue
2019
Zenodo
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Thereapplicationhighlightsthere-useofCWLtooldescriptions and the outputs of the Compute (WP4) and Interoperability platforms (WP5), and demonstrates how workflows can be used to make new data resources ...
This new resource dramatically increases the representation of micro-eukaryotic organisms, both in this new database, as well as being propagated to core data resources such as ENA and UniProtKB. ...
Task 6.2 will be achieved by establishing marine microbial databases including reference genomes, nucleotide and protein databases. ...
doi:10.5281/zenodo.3234521
fatcat:hd3lxdjedjbldothtk5mz26wue
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